"Failed to set trace monitor for deviance There are no observed stochastic nodes" error wh-CodePudding

I'm trying to get an N-mixture model to run in JAGS for a stats class that I'm currently in. However, I keep getting the error "Failed to set trace monitor for deviance There are no observed stochastic nodes" whenever I try to run the model. At the moment I'm just trying to get a very basic model with no covariates to run to make sure I have everything formatted correctly but am still unable to get the model to run. Any advice would be very much appreciated as I've been struggling with this for a while now and can't figure out where I've gone wrong.

Here's a reproducible example of the issue:

library(R2jags)

# Create example dataframe

years <- c(1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2)
sites <- c(1,1,1,2,2,2,3,3,3,1,1,1,2,2,2,3,3,3)
months <- c(1,2,3,1,2,3,1,2,3,1,2,3,1,2,3,1,2,3)

# Detection data
day1 <- floor(runif(18,0,7))
day2 <- floor(runif(18,0,7))
day3 <- floor(runif(18,0,7))
day4 <- floor(runif(18,0,7))
day5 <- floor(runif(18,0,7))

df <- as.data.frame(cbind(years, sites, months, day1, day2, day3, day4, day5))


# Put data into array
y <- array(NA,dim=c(2,3,3,5))                

for(m in 1:2){
  for(k in 1:3){
    sel.rows <- df$years == m & 
      df$months==k
    y[m,k,,] <- as.matrix(df)[sel.rows,4:8]
  }
}

# JAGS model
sink("model1.txt")
cat("
    model {
    
    # PRIORS

     lambda ~ dunif(0,10)
     p ~ dunif(0,1)
    
    # LIKELIHOOD
    # ECOLOGICAL MODEL FOR TRUE ABUNDANCE
      for (m in 1:2) {                            # Loop over years (1-2)
        
        for (k in 1:3) {                          # Loop over months (1-3)
        
          for (i in 1:3) {                        # Loop over sites (1-3)
    
            N[m,k,i] ~ dpois(lambda)              
    
            for (j in 1:5) {                     # Loop over days (1-5)
            
              y[m,k,i,j] ~ dbin(p, N[m,k,i])   
                                                      
            }#j
          }#i
        }#k
      }#m
  }#END", fill=TRUE)
sink()

win.data <- list(y <- y)

Nst <- apply(y,c(1,2,3),max) 1

inits <- function()list(N = Nst)

params <- c("lambda",
            "N") 

nc <- 3
nt <- 1
ni <- 5000
nb <- 500

out <- jags(win.data, inits, params, "model1.txt", 
             n.chains = nc, n.thin = nt, n.iter = ni, n.burnin = nb, 
             working.directory = getwd())

CodePudding user response：

Inside of list objects you cannot use the "<-" assignment operator to create a named list, which is what you need to provide to JAGS. Instead, you need to use =.

So if you change this line in your code:

# this line
win.data <- list(y <- y)

to:

win.data <- list(y = y)

the model compiles.